Monday, November 18, 2019

ThermoRawFileParser --- A big little step away from Windows!

A long time ago I was in a relatively serious car accident. My recovery cost me two weeks of classes and I learned that concussions are seriously no fun at all. However, if you gave me an option of going through that again or migrating all my computers to Windows 10....I'd need time to think about it.

Unfortunately, like all of us, there is no choice at all. Windows 10 support is ending and our field is intrinsically tied to this Cortana and Bing infused catastrophe. Or is it? What is still missing?

Sure -- the instruments need to run on a corporate operating system but there are increasing numbers of options for the data processing that don't involve somoeone running an ad to try and sell you stuff while looking for your stuff on your hard drive

(If you do run into an Ad inside your computer, this tutorial will help. This appears disabled in Enterprise versions, but who knows for how long? I removed Cortana from the SysReg manually, and on the next update, there she is, helpfully taking me to a place to purchase Kanye's new album every time I type the exact name of an Excel spreadsheet into the search bar.

"..thanks Bing! You're the best!"

I should sleep more. This is getting out of hand.

Certain bioinformaticians in our field have been leading the charge away from Windows for quite some time and my obsession with learning how to follow them is filling the pages of this increasingly strange blog these days. And ThermoRAWFileParser couldn't have come at a better time!

I'm working on installing the ProteoWizard on our cluster now, and as far as I can tell there is still considerable extra functionality in it that I should definitely still get both up there, but this new tool has some really cool advantages as well, including the direct production of JSON metadata files. And, in a head to head with msConvert, it appears the new tool produces mzML files more accurately, as they result in more total peptide IDs!

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